What happens if you don't send the tracking signal?

[Zach055]

Does Phineas still get captured? How did the board react to you betraying them? Does it affect the story at all?

[Du-Vu]

He does still get captured, that's inevitable. Some dialogue changes with the adjutant and/or the chairman depending on if the adjutant is still alive, and the Board lose more of their troops in securing Phineas, especially if you warn him.